Sandbox 201: Difference between revisions
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:The enzyme binds <scene name='Sandbox_201/Ca/1'>four calcium ions</scene> Ca<sup>2+</sup>. <scene name='Sandbox_201/Ca6_apc_residues/1'>Two</scene> are coordinated to six water molecules. They do not directly interact with the enzyme, but via water molecules interacting with Glu227, Glu159, Lys99, Glu100, and Tyr246 via hydrogen bonds. They also interact with one phosphoryl oxygen of the AMPcPP. <scene name='Sandbox_201/Ca4_residues/2'>Two other</scene> are coordinated to four water molecules and interact with three enzyme residues (Ile211 and Asp212) via hydrogen bonds. | :The enzyme binds <scene name='Sandbox_201/Ca/1'>four calcium ions</scene> Ca<sup>2+</sup>. <scene name='Sandbox_201/Ca6_apc_residues/1'>Two</scene> are coordinated to six water molecules. They do not directly interact with the enzyme, but via water molecules interacting with Glu227, Glu159, Lys99, Glu100, and Tyr246 via hydrogen bonds. They also interact with one phosphoryl oxygen of the AMPcPP. <scene name='Sandbox_201/Ca4_residues/2'>Two other</scene> are coordinated to four water molecules and interact with three enzyme residues (Ile211 and Asp212) via hydrogen bonds. | ||
:Calcium is very important for enzyme Rnl1 structural biology, because the enzyme crystallizes only in présence of Ca<sup>2+</sup>. This could be explained by the fact that interactions between Ca<sup>2+</sup> and negatively charged surface of each Rnl1 allow interactions between several enzymes at crystallization interfaces.<ref name="main_article" /> | :Calcium is very important for enzyme Rnl1 structural biology, because the enzyme crystallizes only in présence of Ca<sup>2+</sup>. This could be explained by the fact that interactions between Ca<sup>2+</sup> and negatively charged surface of each Rnl1 allow interactions between several enzymes at crystallization interfaces.<ref name="main_article" /> | ||
* RNA binding site | * RNA binding site | ||
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* AMPcPP binding site | * AMPcPP binding site | ||
:T4 RNA ligase can bind two AMPcPP. This molecule does not allow the nucleotidyltransferase function of the enzyme, but it seems necessary to Rnl1 cristallyzation. Each AMPcPP interacts via hydrogen bonds with ten residues (Tyr37, Arg54, Lys75, Tyr98, Lys99, Glu100, Lys119, Glu159, Lys 240 and Lys242), one Ca<sup>2+</sup>, one Mg<sup>2+</sup> one Cl<sup>-</sup>. It also interacts with several other enzyme residues via hydrophobic interactions. | :T4 RNA ligase can bind two AMPcPP. This molecule does not allow the nucleotidyltransferase function of the enzyme, but it seems necessary to Rnl1 cristallyzation. Each AMPcPP interacts via hydrogen bonds with ten residues (Tyr37, Arg54, Lys75, Tyr98, Lys99, Glu100, Lys119, Glu159, Lys 240 and Lys242), one Ca<sup>2+</sup>, one Mg<sup>2+</sup> and one Cl<sup>-</sup>. It also interacts with several other enzyme residues via hydrophobic interactions. | ||
</StructureSection> | </StructureSection> | ||
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==Chemical reaction== | ==Chemical reaction== | ||
The T4 RNA ligase catalyzes the formation of phosphodiester bonds between the 5'-phosphate terminus of single-stranded nucleic acid i and the 3'-hydroxyl terminus of single-stranded nucleic acid j. | The T4 RNA ligase catalyzes the formation of phosphodiester bonds between the 5'-phosphate terminus of single-stranded nucleic acid (i) and the 3'-hydroxyl terminus of single-stranded nucleic acid (j). | ||
ATP + ribonucleotide<sub>(i)</sub> + ribonucleotide<sub>(j)</sub> → AMP + diphosphate + ribonucleotide<sub>(i+j)</sub> | ATP + ribonucleotide<sub>(i)</sub> + ribonucleotide<sub>(j)</sub> → AMP + diphosphate + ribonucleotide<sub>(i+j)</sub> | ||
